1
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Kawaguchi A, Wang J, Knapp D, Murawala P, Nowoshilow S, Masselink W, Taniguchi-Sugiura Y, Fei JF, Tanaka EM. A chromatin code for limb segment identity in axolotl limb regeneration. Dev Cell 2024:S1534-5807(24)00300-9. [PMID: 38788714 DOI: 10.1016/j.devcel.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 07/25/2023] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
The salamander limb correctly regenerates missing limb segments because connective tissue cells have segment-specific identities, termed "positional information". How positional information is molecularly encoded at the chromatin level has been unknown. Here, we performed genome-wide chromatin profiling in mature and regenerating axolotl limb connective tissue cells. We find segment-specific levels of histone H3K27me3 as the major positional mark, especially at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. In the hand, the permissive chromatin state of the homeoprotein gene HoxA13 engages with the regeneration program bypassing the upper limb program. Comparison of regeneration regulatory elements with those found in other regenerative animals identified a core shared set of transcription factors, supporting an ancient, conserved regeneration program.
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Affiliation(s)
- Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dunja Knapp
- DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Sergej Nowoshilow
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; DFG Research Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
| | - Wouter Masselink
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Yuka Taniguchi-Sugiura
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
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2
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Ando K, Ou J, Thompson JD, Welsby J, Bangru S, Shen J, Wei X, Diao Y, Poss KD. A screen for regeneration-associated silencer regulatory elements in zebrafish. Dev Cell 2024; 59:676-691.e5. [PMID: 38290519 PMCID: PMC10939760 DOI: 10.1016/j.devcel.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Regeneration involves gene expression changes explained in part by context-dependent recruitment of transcriptional activators to distal enhancers. Silencers that engage repressive transcriptional complexes are less studied than enhancers and more technically challenging to validate, but they potentially have profound biological importance for regeneration. Here, we identified candidate silencers through a screening process that examined the ability of DNA sequences to limit injury-induced gene expression in larval zebrafish after fin amputation. A short sequence (s1) on chromosome 5 near several genes that reduce expression during adult fin regeneration could suppress promoter activity in stable transgenic lines and diminish nearby gene expression in knockin lines. High-resolution analysis of chromatin organization identified physical associations of s1 with gene promoters occurring preferentially during fin regeneration, and genomic deletion of s1 elevated the expression of these genes after fin amputation. Our study provides methods to identify "tissue regeneration silencer elements" (TRSEs) with the potential to reduce unnecessary or deleterious gene expression during regeneration.
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Affiliation(s)
- Kazunori Ando
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jianhong Ou
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John D Thompson
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John Welsby
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sushant Bangru
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jingwen Shen
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaolin Wei
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yarui Diao
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D Poss
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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3
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Shin K, Begeman IJ, Cao J, Kang J. leptin b and its regeneration enhancer illustrate the regenerative features of zebrafish hearts. Dev Dyn 2024; 253:91-106. [PMID: 36495292 PMCID: PMC10256838 DOI: 10.1002/dvdy.556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/11/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Zebrafish possess a remarkable regenerative capacity, which is mediated by the induction of various genes upon injury. Injury-dependent transcription is governed by the tissue regeneration enhancer elements (TREEs). Here, we utilized leptin b (lepb), an injury-specific factor, and its TREE to dissect heterogeneity of noncardiomyocytes (CMs) in regenerating hearts. RESULTS Our single-cell RNA sequencing (scRNA-seq) analysis demonstrated that the endothelium/endocardium(EC) is activated to induce distinct subpopulations upon injury. We demonstrated that lepb can be utilized as a regeneration-specific marker to subset injury-activated ECs. lepb+ ECs robustly induce pro-regenerative factors, implicating lepb+ ECs as a signaling center to interact with other cardiac cells. Our scRNA-seq analysis identified that lepb is also produced by subpopulation of epicardium (Epi) and epicardium-derived cells (EPDCs). To determine whether lepb labels injury-emerging non-CM cells, we tested the activity of lepb-linked regeneration enhancer (LEN) with chromatin accessibility profiles and transgenic lines. While nondetectable in uninjured hearts, LEN directs EC and Epi/EPDC expression upon injury. The endogenous LEN activity was assessed using LEN deletion lines, demonstrating that LEN deletion abolished injury-dependent expression of lepb, but not other nearby genes. CONCLUSIONS Our integrative analyses identify regeneration-emerging cell-types and factors, leading to the discovery of regenerative features of hearts.
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Affiliation(s)
- Kwangdeok Shin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI, 53705, USA
| | - Ian J. Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI, 53705, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10021, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI, 53705, USA
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4
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Rao A, Lyu B, Jahan I, Lubertozzi A, Zhou G, Tedeschi F, Jankowsky E, Kang J, Carstens B, Poss KD, Baskin K, Goldman JA. The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration. Development 2023; 150:dev201376. [PMID: 37306388 PMCID: PMC10281269 DOI: 10.1242/dev.201376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
The eIF4E family of translation initiation factors bind 5' methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c, for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting that Eif4e1c functions in a novel pathway. Deletion of eif4e1c in zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although eif4e1c is broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
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Affiliation(s)
- Anupama Rao
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Baken Lyu
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Ishrat Jahan
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Anna Lubertozzi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Gao Zhou
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Frank Tedeschi
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bryan Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kedryn Baskin
- Department of Cell Biology and Physiology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Joseph Aaron Goldman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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5
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Cigliola V, Shoffner A, Lee N, Ou J, Gonzalez TJ, Hoque J, Becker CJ, Han Y, Shen G, Faw TD, Abd-El-Barr MM, Varghese S, Asokan A, Poss KD. Spinal cord repair is modulated by the neurogenic factor Hb-egf under direction of a regeneration-associated enhancer. Nat Commun 2023; 14:4857. [PMID: 37567873 PMCID: PMC10421883 DOI: 10.1038/s41467-023-40486-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Unlike adult mammals, zebrafish regenerate spinal cord tissue and recover locomotor ability after a paralyzing injury. Here, we find that ependymal cells in zebrafish spinal cords produce the neurogenic factor Hb-egfa upon transection injury. Animals with hb-egfa mutations display defective swim capacity, axon crossing, and tissue bridging after spinal cord transection, associated with disrupted indicators of neuron production. Local recombinant human HB-EGF delivery alters ependymal cell cycling and tissue bridging, enhancing functional regeneration. Epigenetic profiling reveals a tissue regeneration enhancer element (TREE) linked to hb-egfa that directs gene expression in spinal cord injuries. Systemically delivered recombinant AAVs containing this zebrafish TREE target gene expression to crush injuries of neonatal, but not adult, murine spinal cords. Moreover, enhancer-based HB-EGF delivery by AAV administration improves axon densities after crush injury in neonatal cords. Our results identify Hb-egf as a neurogenic factor necessary for innate spinal cord regeneration and suggest strategies to improve spinal cord repair in mammals.
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Affiliation(s)
- Valentina Cigliola
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Université Côte d'Azur, Inserm, CNRS, Institut de Biologie Valrose, Nice, France
| | - Adam Shoffner
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Nutishia Lee
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Jianhong Ou
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Trevor J Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Jiaul Hoque
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Clayton J Becker
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Yanchao Han
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, Soochow University, Suzhou, Jiangsu, China
| | - Grace Shen
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Timothy D Faw
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | | | - Shyni Varghese
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Aravind Asokan
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Kenneth D Poss
- Duke Regeneration Center, Duke University, Durham, NC, USA.
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
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6
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Jimenez Gonzalez A, Baranasic D, Müller F. Zebrafish regulatory genomic resources for disease modelling and regeneration. Dis Model Mech 2023; 16:dmm050280. [PMID: 37529920 PMCID: PMC10417509 DOI: 10.1242/dmm.050280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
In the past decades, the zebrafish has become a disease model with increasing popularity owing to its advantages that include fast development, easy genetic manipulation, simplicity for imaging, and sharing conserved disease-associated genes and pathways with those of human. In parallel, studies of disease mechanisms are increasingly focusing on non-coding mutations, which require genome annotation maps of regulatory elements, such as enhancers and promoters. In line with this, genomic resources for zebrafish research are expanding, producing a variety of genomic data that help in defining regulatory elements and their conservation between zebrafish and humans. Here, we discuss recent developments in generating functional annotation maps for regulatory elements of the zebrafish genome and how this can be applied to human diseases. We highlight community-driven developments, such as DANIO-CODE, in generating a centralised and standardised catalogue of zebrafish genomics data and functional annotations; consider the advantages and limitations of current annotation maps; and offer considerations for interpreting and integrating existing maps with comparative genomics tools. We also discuss the need for developing standardised genomics protocols and bioinformatic pipelines and provide suggestions for the development of analysis and visualisation tools that will integrate various multiomic bulk sequencing data together with fast-expanding data on single-cell methods, such as single-cell assay for transposase-accessible chromatin with sequencing. Such integration tools are essential to exploit the multiomic chromatin characterisation offered by bulk genomics together with the cell-type resolution offered by emerging single-cell methods. Together, these advances will build an expansive toolkit for interrogating the mechanisms of human disease in zebrafish.
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Affiliation(s)
- Ada Jimenez Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London SW7 2AZ, UK
- MRC London Institute of Medical Sciences, London W12 0NN, UK
- Division of Electronics, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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7
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Tamaki T, Yoshida T, Shibata E, Nishihara H, Ochi H, Kawakami A. Splashed E-box and AP-1 motifs cooperatively drive regeneration response and shape regeneration abilities. Biol Open 2023; 12:286596. [PMID: 36636913 PMCID: PMC9922731 DOI: 10.1242/bio.059810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
Injury triggers a genetic program that induces gene expression for regeneration. Recent studies have identified regeneration-response enhancers (RREs); however, it remains unclear whether a common mechanism operates in these RREs. We identified three RREs from the zebrafish fn1b promoter by searching for conserved sequences within the surrounding genomic regions of regeneration-induced genes and performed a transgenic assay for regeneration response. Two regions contained in the transposons displayed RRE activity when combined with the -0.7 kb fn1b promoter. Another non-transposon element functioned as a stand-alone enhancer in combination with a minimum promoter. By searching for transcription factor-binding motifs and validation by transgenic assays, we revealed that the cooperation of E-box and activator protein 1 motifs is necessary and sufficient for regenerative response. Such RREs respond to variety of tissue injuries, including those in the zebrafish heart and Xenopus limb buds. Our findings suggest that the fidelity of regeneration response is ensured by the two signals evoked by tissue injuries. It is speculated that a large pool of potential enhancers in the genome has helped shape the regenerative capacities during evolution.
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Affiliation(s)
- Teruhisa Tamaki
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Takafumi Yoshida
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Eri Shibata
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata, Yamagata Pref. 990-9585, Japan
| | - Atsushi Kawakami
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan,Author for correspondence ()
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8
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Wnt/β-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration. Nat Commun 2023; 14:298. [PMID: 36653403 PMCID: PMC9849279 DOI: 10.1038/s41467-023-35937-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
For successful regeneration, the identity of the missing tissue must be specified according to the pre-existing tissue. Planarians are ideal for the study of the mechanisms underlying this process; the same field of cells can regrow a head or a tail according to the missing body part. After amputation, the differential activation of the Wnt/β-catenin signal specifies anterior versus posterior identity. Initially, both wnt1 and notum (Wnt inhibitor) are expressed in all wounds, but 48 hours later they are restricted to posterior or anterior facing wounds, respectively, by an unknown mechanism. Here we show that 12 hours after amputation, the chromatin accessibility of cells in the wound region changes according to the polarity of the pre-existing tissue in a Wnt/β-catenin-dependent manner. Genomic analyses suggest that homeobox transcription factors and chromatin-remodeling proteins are direct Wnt/β-catenin targets, which trigger the expression of posterior effectors. Finally, we identify FoxG as a wnt1 up-stream regulator, probably via binding to its first intron enhancer region.
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9
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Yan R, Cigliola V, Oonk KA, Petrover Z, DeLuca S, Wolfson DW, Vekstein A, Mendiola MA, Devlin G, Bishawi M, Gemberling MP, Sinha T, Sargent MA, York AJ, Shakked A, DeBenedittis P, Wendell DC, Ou J, Kang J, Goldman JA, Baht GS, Karra R, Williams AR, Bowles DE, Asokan A, Tzahor E, Gersbach CA, Molkentin JD, Bursac N, Black BL, Poss KD. An enhancer-based gene-therapy strategy for spatiotemporal control of cargoes during tissue repair. Cell Stem Cell 2023; 30:96-111.e6. [PMID: 36516837 PMCID: PMC9830588 DOI: 10.1016/j.stem.2022.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 10/06/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022]
Abstract
The efficacy and safety of gene-therapy strategies for indications like tissue damage hinge on precision; yet, current methods afford little spatial or temporal control of payload delivery. Here, we find that tissue-regeneration enhancer elements (TREEs) isolated from zebrafish can direct targeted, injury-associated gene expression from viral DNA vectors delivered systemically in small and large adult mammalian species. When employed in combination with CRISPR-based epigenome editing tools in mice, zebrafish TREEs stimulated or repressed the expression of endogenous genes after ischemic myocardial infarction. Intravenously delivered recombinant AAV vectors designed with a TREE to direct a constitutively active YAP factor boosted indicators of cardiac regeneration in mice and improved the function of the injured heart. Our findings establish the application of contextual enhancer elements as a potential therapeutic platform for spatiotemporally controlled tissue regeneration in mammals.
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Affiliation(s)
- Ruorong Yan
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA
| | - Valentina Cigliola
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA
| | - Kelsey A Oonk
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA
| | - Zachary Petrover
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sophia DeLuca
- Department of Cell Biology, Duke University Medical School, Durham, NC, USA; Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - David W Wolfson
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Andrew Vekstein
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Garth Devlin
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Muath Bishawi
- Department of Biomedical Engineering, Duke University, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Matthew P Gemberling
- Department of Biomedical Engineering, Duke University, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Tanvi Sinha
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Michelle A Sargent
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Allen J York
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Avraham Shakked
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - David C Wendell
- Duke Cardiovascular Magnetic Resonance Center, Duke University Medical Center, Durham, NC, USA
| | - Jianhong Ou
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Joseph A Goldman
- Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA
| | - Gurpreet S Baht
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA; Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Ravi Karra
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Adam R Williams
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Dawn E Bowles
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Aravind Asokan
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Biomedical Engineering, Duke University, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Eldad Tzahor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Charles A Gersbach
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA; Department of Biomedical Engineering, Duke University, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA; Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Jeffery D Molkentin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kenneth D Poss
- Duke Regeneration Center, Duke University, Durham, NC, USA; Department of Cell Biology, Duke University Medical School, Durham, NC, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
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10
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Erhardt S, Wang J. Cardiac Neural Crest and Cardiac Regeneration. Cells 2022; 12:cells12010111. [PMID: 36611905 PMCID: PMC9818523 DOI: 10.3390/cells12010111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022] Open
Abstract
Neural crest cells (NCCs) are a vertebrate-specific, multipotent stem cell population that have the ability to migrate and differentiate into various cell populations throughout the embryo during embryogenesis. The heart is a muscular and complex organ whose primary function is to pump blood and nutrients throughout the body. Mammalian hearts, such as those of humans, lose their regenerative ability shortly after birth. However, a few vertebrate species, such as zebrafish, have the ability to self-repair/regenerate after cardiac damage. Recent research has discovered the potential functional ability and contribution of cardiac NCCs to cardiac regeneration through the use of various vertebrate species and pluripotent stem cell-derived NCCs. Here, we review the neural crest's regenerative capacity in various tissues and organs, and in particular, we summarize the characteristics of cardiac NCCs between species and their roles in cardiac regeneration. We further discuss emerging and future work to determine the potential contributions of NCCs for disease treatment.
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Affiliation(s)
- Shannon Erhardt
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas, Houston, TX 77030, USA
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas, Houston, TX 77030, USA
- Correspondence:
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11
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Harris RE. Regeneration enhancers: a field in development. Am J Physiol Cell Physiol 2022; 323:C1548-C1554. [PMID: 36252130 PMCID: PMC9829460 DOI: 10.1152/ajpcell.00403.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ability to regenerate tissues and organs following damage is not equally distributed across metazoans, and even highly related species can vary considerably in their regenerative capacity. Studies of animals with high regenerative potential have shown that factors expressed during normal development are often reactivated upon damage and required for successful regeneration. As such, regenerative potential may not be dictated by the presence or absence of the necessary genes, but whether such genes are appropriately activated following injury. The identification of damage-responsive enhancers that regulate regenerative gene expression in multiple species and tissues provides possible mechanistic insight into this phenomenon. Enhancers that are reused from developmental programs, and those that are potentially unique to regeneration, have been characterized individually and at a genome-wide scale. A better understanding of the regulatory events that, direct and in some cases limit, regenerative capacity is an important step in developing new methods to manipulate and augment regeneration, particularly in tissues that do not have this ability, including those of humans.
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Affiliation(s)
- Robin E. Harris
- School of Life Sciences, Arizona State University, Tempe, Arizona
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12
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Adrenergic receptor signaling induced by Klf15, a regulator of regeneration enhancer, promotes kidney reconstruction. Proc Natl Acad Sci U S A 2022; 119:e2204338119. [PMID: 35939709 PMCID: PMC9388080 DOI: 10.1073/pnas.2204338119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the recent discovery of tissue regeneration enhancers in highly regenerative animals, upstream and downstream genetic programs connected by these enhancers still remain unclear. Here, we performed a genome-wide analysis of enhancers and associated genes in regenerating nephric tubules of Xenopus laevis. Putative enhancers were identified using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) analyses. Their target genes were predicted based on their proximity to enhancers on genomic DNA and consistency of their transcriptome profiles to ATAC-seq/ChIP-seq profiles of the enhancers. Motif enrichment analysis identified the central role of Krüppel-like factors (Klf) in the enhancer. Klf15, a member of the Klf family, directly binds enhancers and stimulates expression of regenerative genes, including adrenoreceptor alpha 1A (adra1a), whereas inhibition of Klf15 activity results in failure of nephric tubule regeneration. Moreover, pharmacological inhibition of Adra1a-signaling suppresses nephric tubule regeneration, while its activation promotes nephric tubule regeneration and restores organ size. These results indicate that Klf15-dependent adrenergic receptor signaling through regeneration enhancers plays a central role in the genetic network for kidney regeneration.
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13
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Osorio-Méndez D, Miller A, Begeman IJ, Kurth A, Hagle R, Rolph D, Dickson AL, Chen CH, Halloran M, Poss KD, Kang J. Voltage-gated sodium channel scn8a is required for innervation and regeneration of amputated adult zebrafish fins. Proc Natl Acad Sci U S A 2022; 119:e2200342119. [PMID: 35867745 PMCID: PMC9282381 DOI: 10.1073/pnas.2200342119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Teleost fishes and urodele amphibians can regenerate amputated appendages, whereas this ability is restricted to digit tips in adult mammals. One key component of appendage regeneration is reinnervation of the wound area. However, how innervation is regulated in injured appendages of adult vertebrates has seen limited research attention. From a forward genetics screen for temperature-sensitive defects in zebrafish fin regeneration, we identified a mutation that disrupted regeneration while also inducing paralysis at the restrictive temperature. Genetic mapping and complementation tests identify a mutation in the major neuronal voltage-gated sodium channel (VGSC) gene scn8ab. Conditional disruption of scn8ab impairs early regenerative events, including blastema formation, but does not affect morphogenesis of established regenerates. Whereas scn8ab mutations reduced neural activity as expected, they also disrupted axon regrowth and patterning in fin regenerates, resulting in hypoinnervation. Our findings indicate that the activity of VGSCs plays a proregenerative role by promoting innervation of appendage stumps.
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Affiliation(s)
- Daniel Osorio-Méndez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Andrew Miller
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705
| | - Ian J. Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Ryan Hagle
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Daniela Rolph
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Amy L. Dickson
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Chen-Hui Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Mary Halloran
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705
| | - Kenneth D. Poss
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
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14
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Sehring I, Weidinger G. Zebrafish Fin: Complex Molecular Interactions and Cellular Mechanisms Guiding Regeneration. Cold Spring Harb Perspect Biol 2022; 14:a040758. [PMID: 34649924 PMCID: PMC9248819 DOI: 10.1101/cshperspect.a040758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The zebrafish caudal fin has become a popular model to study cellular and molecular mechanisms of regeneration due to its high regenerative capacity, accessibility for experimental manipulations, and relatively simple anatomy. The formation of a regenerative epidermis and blastema are crucial initial events and tightly regulated. Both the regenerative epidermis and the blastema are highly organized structures containing distinct domains, and several signaling pathways regulate the formation and interaction of these domains. Bone is the major tissue regenerated from the progenitor cells of the blastema. Several cellular mechanisms can provide source cells for blastemal (pre-)osteoblasts, including dedifferentiation of differentiated osteoblasts and de novo formation from other cell types, providing intriguing examples of cellular plasticity. In recent years, omics analyses and single-cell approaches have elucidated genetic and epigenetic regulation, increasing our knowledge of the surprisingly complex coordination of various mechanisms to achieve successful restoration of a seemingly simple structure.
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Affiliation(s)
- Ivonne Sehring
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Gilbert Weidinger
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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15
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Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements. Biochem Soc Trans 2022; 50:1167-1177. [PMID: 35604124 PMCID: PMC9246326 DOI: 10.1042/bst20210834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022]
Abstract
Mapping accessible chromatin across time scales can give insights into its dynamic nature, for example during cellular differentiation and tissue or organism development. Analysis of such data can be utilised to identify functional cis-regulatory elements (CRE) and transcription factor binding sites and, when combined with transcriptomics, can reveal gene regulatory networks (GRNs) of expressed genes. Chromatin accessibility mapping is a powerful approach and can be performed using ATAC-sequencing (ATAC-seq), whereby Tn5 transposase inserts sequencing adaptors into genomic DNA to identify differentially accessible regions of chromatin in different cell populations. It requires low sample input and can be performed and analysed relatively quickly compared with other methods. The data generated from ATAC-seq, along with other genomic approaches, can help uncover chromatin packaging and potential cis-regulatory elements that may be responsible for gene expression. Here, we describe the ATAC-seq approach and give examples from mainly vertebrate embryonic development, where such datasets have identified the highly dynamic nature of chromatin, with differing landscapes between cellular precursors for different lineages.
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16
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Sun F, Ou J, Shoffner AR, Luan Y, Yang H, Song L, Safi A, Cao J, Yue F, Crawford GE, Poss KD. Enhancer selection dictates gene expression responses in remote organs during tissue regeneration. Nat Cell Biol 2022; 24:685-696. [PMID: 35513710 DOI: 10.1038/s41556-022-00906-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
Abstract
Acute trauma stimulates local repair mechanisms but can also impact structures distant from the injury, for example through the activity of circulating factors. To study the responses of remote tissues during tissue regeneration, we profiled transcriptomes of zebrafish brains after experimental cardiac damage. We found that the transcription factor gene cebpd was upregulated remotely in brain ependymal cells as well as kidney tubular cells, in addition to its local induction in epicardial cells. cebpd mutations altered both local and distant cardiac injury responses, altering the cycling of epicardial cells as well as exchange between distant fluid compartments. Genome-wide profiling and transgenesis identified a hormone-responsive enhancer near cebpd that exists in a permissive state, enabling rapid gene expression in heart, brain and kidney after cardiac injury. Deletion of this sequence selectively abolished cebpd induction in remote tissues and disrupted fluid regulation after injury, without affecting its local cardiac expression response. Our findings suggest a model to broaden gene function during regeneration in which enhancer regulatory elements define short- and long-range expression responses to injury.
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Affiliation(s)
- Fei Sun
- Duke Regeneration Center, Duke University, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Jianhong Ou
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Adam R Shoffner
- Duke Regeneration Center, Duke University, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medical College, New York, NY, USA.,Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Kenneth D Poss
- Duke Regeneration Center, Duke University, Durham, NC, USA. .,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
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17
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mdka Expression Is Associated with Quiescent Neural Stem Cells during Constitutive and Reactive Neurogenesis in the Adult Zebrafish Telencephalon. Brain Sci 2022; 12:brainsci12020284. [PMID: 35204047 PMCID: PMC8870249 DOI: 10.3390/brainsci12020284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/09/2022] [Accepted: 02/16/2022] [Indexed: 12/27/2022] Open
Abstract
In contrast to mammals, adult zebrafish display an extraordinary capacity to heal injuries and repair damage in the central nervous system. Pivotal for the regenerative capacity of the zebrafish brain at adult stages is the precise control of neural stem cell (NSC) behavior and the maintenance of the stem cell pool. The gene mdka, a member of a small family of heparin binding growth factors, was previously shown to be involved in regeneration in the zebrafish retina, heart, and fin. Here, we investigated the expression pattern of the gene mdka and its paralogue mdkb in the zebrafish adult telencephalon under constitutive and regenerative conditions. Our findings show that only mdka expression is specifically restricted to the telencephalic ventricle, a stem cell niche of the zebrafish telencephalon. In this brain region, mdka is particularly expressed in the quiescent stem cells. Interestingly, after brain injury, mdka expression remains restricted to the resting stem cell, which might suggest a role of mdka in regulating stem cell quiescence.
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18
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Cao Y, Xia Y, Balowski JJ, Ou J, Song L, Safi A, Curtis T, Crawford GE, Poss KD, Cao J. Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration. Development 2022; 149:274414. [PMID: 35179181 PMCID: PMC8918790 DOI: 10.1242/dev.200133] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/11/2022] [Indexed: 12/17/2022]
Abstract
The epicardium is a mesothelial tissue layer that envelops the heart. Cardiac injury activates dynamic gene expression programs in epicardial tissue, which in zebrafish enables subsequent regeneration through paracrine and vascularizing effects. To identify tissue regeneration enhancer elements (TREEs) that control injury-induced epicardial gene expression during heart regeneration, we profiled transcriptomes and chromatin accessibility in epicardial cells purified from regenerating zebrafish hearts. We identified hundreds of candidate TREEs, which are defined by increased chromatin accessibility of non-coding elements near genes with increased expression during regeneration. Several of these candidate TREEs were incorporated into stable transgenic lines, with five out of six elements directing injury-induced epicardial expression but not ontogenetic epicardial expression in larval hearts. Whereas two independent TREEs linked to the gene gnai3 showed similar functional features of gene regulation in transgenic lines, two independent ncam1a-linked TREEs directed distinct spatiotemporal domains of epicardial gene expression. Thus, multiple TREEs linked to a regeneration gene can possess either matching or complementary regulatory controls. Our study provides a new resource and principles for understanding the regulation of epicardial genetic programs during heart regeneration. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Yingxi Cao
- Cardiovascular Research Institute, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA,Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
| | - Yu Xia
- Cardiovascular Research Institute, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA,Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
| | - Joseph J. Balowski
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA,Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Jianhong Ou
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA,Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA,Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA,Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy Curtis
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA,Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Gregory E. Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA,Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA,Duke Regeneration Center, Duke University, Durham, NC 27710, USA,Authors for correspondence (; )
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA,Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA,Authors for correspondence (; )
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19
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Leigh ND, Currie JD. Re-building limbs, one cell at a time. Dev Dyn 2022; 251:1389-1403. [PMID: 35170828 PMCID: PMC9545806 DOI: 10.1002/dvdy.463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
New techniques for visualizing and interrogating single cells hold the key to unlocking the underlying mechanisms of salamander limb regeneration.
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Affiliation(s)
- Nicholas D Leigh
- Molecular Medicine and Gene Therapy, Wallenberg Centre for Molecular Medicine, Lund Stem Cell Center, Lund University, Sweden
| | - Joshua D Currie
- Department of Biology, Wake Forest University, 455 Vine Street, Winston-Salem, USA
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20
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Riley SE, Feng Y, Hansen CG. Hippo-Yap/Taz signalling in zebrafish regeneration. NPJ Regen Med 2022; 7:9. [PMID: 35087046 PMCID: PMC8795407 DOI: 10.1038/s41536-022-00209-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/14/2021] [Indexed: 12/29/2022] Open
Abstract
The extent of tissue regeneration varies widely between species. Mammals have a limited regenerative capacity whilst lower vertebrates such as the zebrafish (Danio rerio), a freshwater teleost, can robustly regenerate a range of tissues, including the spinal cord, heart, and fin. The molecular and cellular basis of this altered response is one of intense investigation. In this review, we summarise the current understanding of the association between zebrafish regeneration and Hippo pathway function, a phosphorylation cascade that regulates cell proliferation, mechanotransduction, stem cell fate, and tumorigenesis, amongst others. We also compare this function to Hippo pathway activity in the regenerative response of other species. We find that the Hippo pathway effectors Yap/Taz facilitate zebrafish regeneration and that this appears to be latent in mammals, suggesting that therapeutically promoting precise and temporal YAP/TAZ signalling in humans may enhance regeneration and hence reduce morbidity.
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Affiliation(s)
- Susanna E Riley
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, Queen's Medical Research Institute, Edinburgh bioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Yi Feng
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, Queen's Medical Research Institute, Edinburgh bioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Carsten Gram Hansen
- University of Edinburgh Centre for Inflammation Research, Institute for Regeneration and Repair, Queen's Medical Research Institute, Edinburgh bioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
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21
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Yue Z, Lei M, Paus R, Chuong CM. The global regulatory logic of organ regeneration: circuitry lessons from skin and its appendages. Biol Rev Camb Philos Soc 2021; 96:2573-2583. [PMID: 34145718 PMCID: PMC10874616 DOI: 10.1111/brv.12767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022]
Abstract
In organ regeneration, the regulatory logic at a systems level remains largely unclear. For example, what defines the quantitative threshold to initiate regeneration, and when does the regeneration process come to an end? What leads to the qualitatively different responses of regeneration, which restore the original structure, or to repair which only heals a wound? Here we discuss three examples in skin regeneration: epidermal recovery after radiation damage, hair follicle fate choice after chemotherapy damage, and wound-induced feather regeneration. We propose that the molecular regulatory circuitry is of paramount significance in organ regeneration. It is conceivable that defects in these controlling pathways may lead to failed regeneration and/or organ renewal, and understanding the underlying logic could help to identify novel therapeutic strategies.
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Affiliation(s)
- ZhiCao Yue
- Department of Cell Biology and Medical Genetics, Carson International Cancer Center, Guangdong Key Laboratory for Genome Stability and Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Mingxing Lei
- 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400038, China
| | - Ralf Paus
- Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136, U.S.A
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA, 90033, U.S.A
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22
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Sasidharan V, Sánchez Alvarado A. The Diverse Manifestations of Regeneration and Why We Need to Study Them. Cold Spring Harb Perspect Biol 2021; 14:a040931. [PMID: 34750171 PMCID: PMC9438785 DOI: 10.1101/cshperspect.a040931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
For hundreds of years, the question of why some organisms can regenerate missing body parts while others cannot has remained poorly understood. This has been due in great part to the inability to genetically, molecularly, and cellularly dissect this problem for most of the history of the field. It has only been in the past 20-30 years that important mechanistic advances have been made in methodologies that introduce loss and gain of gene function in animals that can regenerate. However, we still have a very incomplete understanding of how broadly regenerative abilities may be dispersed across species and whether or not such properties share a common evolutionary origin, which may have emerged independently or both. Understanding regeneration, therefore, will require rigorously practiced fundamental, curiosity-driven, discovery research. Expanding the number of research organisms used to study regeneration allows us to uncover aspects of this problem we may not yet know exist and simultaneously increases our chances of solving this long-standing problem of biology.
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23
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Mehta AS, Deshpande P, Chimata AV, Tsonis PA, Singh A. Newt regeneration genes regulate Wingless signaling to restore patterning in Drosophila eye. iScience 2021; 24:103166. [PMID: 34746690 PMCID: PMC8551474 DOI: 10.1016/j.isci.2021.103166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/02/2021] [Accepted: 09/21/2021] [Indexed: 12/21/2022] Open
Abstract
Newts utilize their unique genes to restore missing parts by strategic regulation of conserved signaling pathways. Lack of genetic tools poses challenges to determine the function of such genes. Therefore, we used the Drosophila eye model to demonstrate the potential of 5 unique newt (Notophthalmus viridescens) gene(s), viropana1-viropana5 (vna1-vna5), which were ectopically expressed in L 2 mutant and GMR-hid, GMR-GAL4 eye. L 2 exhibits the loss of ventral half of early eye and head involution defective (hid) triggers cell-death during later eye development. Surprisingly, newt genes significantly restore missing photoreceptor cells both in L 2 and GMR>hid background by upregulating cell-proliferation and blocking cell-death, regulating evolutionarily conserved Wingless (Wg)/Wnt signaling pathway and exhibit non-cell-autonomous rescues. Further, Wg/Wnt signaling acts downstream of newt genes. Our data highlights that unique newt proteins can regulate conserved pathways to trigger a robust restoration of missing photoreceptor cells in Drosophila eye model with weak restoration capability.
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Affiliation(s)
| | | | | | | | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH 45469, USA
- Premedical Program, University of Dayton, Dayton, USA
- Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, USA
- The Integrative Science and Engineering Center, University of Dayton, Dayton, OH 45469, USA
- Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA
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24
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Parisi C, Vashisht S, Winata CL. Fish-Ing for Enhancers in the Heart. Int J Mol Sci 2021; 22:3914. [PMID: 33920121 PMCID: PMC8069060 DOI: 10.3390/ijms22083914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precise control of gene expression is crucial to ensure proper development and biological functioning of an organism. Enhancers are non-coding DNA elements which play an essential role in regulating gene expression. They contain specific sequence motifs serving as binding sites for transcription factors which interact with the basal transcription machinery at their target genes. Heart development is regulated by intricate gene regulatory network ensuring precise spatiotemporal gene expression program. Mutations affecting enhancers have been shown to result in devastating forms of congenital heart defect. Therefore, identifying enhancers implicated in heart biology and understanding their mechanism is key to improve diagnosis and therapeutic options. Despite their crucial role, enhancers are poorly studied, mainly due to a lack of reliable way to identify them and determine their function. Nevertheless, recent technological advances have allowed rapid progress in enhancer discovery. Model organisms such as the zebrafish have contributed significant insights into the genetics of heart development through enabling functional analyses of genes and their regulatory elements in vivo. Here, we summarize the current state of knowledge on heart enhancers gained through studies in model organisms, discuss various approaches to discover and study their function, and finally suggest methods that could further advance research in this field.
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Affiliation(s)
- Costantino Parisi
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Shikha Vashisht
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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25
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Zheng L, Du J, Wang Z, Zhou Q, Zhu X, Xiong JW. Molecular regulation of myocardial proliferation and regeneration. CELL REGENERATION (LONDON, ENGLAND) 2021; 10:13. [PMID: 33821373 PMCID: PMC8021683 DOI: 10.1186/s13619-021-00075-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/04/2021] [Indexed: 12/21/2022]
Abstract
Heart regeneration is a fascinating and complex biological process. Decades of intensive studies have revealed a sophisticated molecular network regulating cardiac regeneration in the zebrafish and neonatal mouse heart. Here, we review both the classical and recent literature on the molecular and cellular mechanisms underlying heart regeneration, with a particular focus on how injury triggers the cell-cycle re-entry of quiescent cardiomyocytes to replenish their massive loss after myocardial infarction or ventricular resection. We highlight several important signaling pathways for cardiomyocyte proliferation and propose a working model of how these injury-induced signals promote cardiomyocyte proliferation. Thus, this concise review provides up-to-date research progresses on heart regeneration for investigators in the field of regeneration biology.
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Affiliation(s)
- Lixia Zheng
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Jianyong Du
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Zihao Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Qinchao Zhou
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Xiaojun Zhu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China.
| | - Jing-Wei Xiong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
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Control of osteoblast regeneration by a train of Erk activity waves. Nature 2021; 590:129-133. [PMID: 33408418 PMCID: PMC7864885 DOI: 10.1038/s41586-020-03085-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/19/2020] [Indexed: 12/27/2022]
Abstract
Regeneration is a complex chain of events that restores a tissue to its original size and shape. The tissue-wide coordination of cellular dynamics needed for proper morphogenesis is challenged by the large dimensions of regenerating body parts. Feedback mechanisms in biochemical pathways can provide effective communication across great distances1-5, but how they might regulate growth during tissue regeneration is unresolved6,7. Here, we report that rhythmic traveling waves of Erk activity control the growth of bone in time and space in regenerating zebrafish scales, millimetre-sized discs of protective body armour. We find that Erk activity waves travel as expanding concentric rings, broadcast from a central source, inducing ring-like patterns of osteoblast tissue growth. Using a combination of theoretical and experimental analyses, we show that Erk activity propagates as excitable trigger waves able to traverse the entire scale in approximately two days, with the frequency of wave generation controlling the rate of scale regeneration. Furthermore, periodic induction of synchronous, tissue-wide Erk activation in place of travelling waves impairs tissue growth, indicating that wave-distributed Erk activation is key to regeneration. Our findings reveal trigger waves as a regulatory strategy to coordinate cell behaviour and instruct tissue form during regeneration.
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Begeman IJ, Shin K, Osorio-Méndez D, Kurth A, Lee N, Chamberlain TJ, Pelegri FJ, Kang J. Decoding an organ regeneration switch by dissecting cardiac regeneration enhancers. Development 2020; 147:226055. [PMID: 33246928 DOI: 10.1242/dev.194019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
Heart regeneration in regeneration-competent organisms can be accomplished through the remodeling of gene expression in response to cardiac injury. This dynamic transcriptional response relies on the activities of tissue regeneration enhancer elements (TREEs); however, the mechanisms underlying TREEs are poorly understood. We dissected a cardiac regeneration enhancer in zebrafish to elucidate the mechanisms governing spatiotemporal gene expression during heart regeneration. Cardiac lepb regeneration enhancer (cLEN) exhibits dynamic, regeneration-dependent activity in the heart. We found that multiple injury-activated regulatory elements are distributed throughout the enhancer region. This analysis also revealed that cardiac regeneration enhancers are not only activated by injury, but surprisingly, they are also actively repressed in the absence of injury. Our data identified a short (22 bp) DNA element containing a key repressive element. Comparative analysis across Danio species indicated that the repressive element is conserved in closely related species. The repression mechanism is not operational during embryogenesis and emerges when the heart begins to mature. Incorporating both activation and repression components into the mechanism of tissue regeneration constitutes a new paradigm that might be extrapolated to other regeneration scenarios.
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Affiliation(s)
- Ian J Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kwangdeok Shin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Daniel Osorio-Méndez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Nutishia Lee
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Francisco J Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
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Abstract
Some lower vertebrates such as zebrafish and axolotl have incredible cardiac regenerative potential while mammals have very limited ones. Comparative studies among species have revealed that cardiomyocyte polyploidy, endothermy, and injury-induced activation of certain transcriptional factors including AP1 complexes are critical for cardiomyocyte proliferation and heart regeneration during animal evolution. Gaining insights into these evolutionarily conserved mechanisms will likely lead to achieving heart regeneration in non-regenerative mammals including humans.
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Affiliation(s)
- Jing-Wei Xiong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China.
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